The current points leader led the majority of the morning, eventually reaching a time of 1m48.131s with his final lap.
Lorenzo's closest challenger ultimately proved to be Casey Stoner. The Honda rider had a quiet start, spending much of the session near the foot of the top 10, before steadily improving his pace to end up half a second down on the Yamaha.
Sachsenring winner Dani Pedrosa lost second to team-mate Stoner late on, but remained third.
The pair were split by Tech 3 Yamaha pair Cal Crutchlow and Andrea Dovizioso, as Crutchlow made it into the top five despite stopping on track with a mechanical problem on his main bike.
Lorenzo's team-mate Ben Spies had a minor fall when he ran wide through the gravel. There was a similar incident for Gresini Honda rider Alvaro Bautista, who tried his utmost to keep his bike running through the San Donato gravel before ultimately having to tip it onto its side.
That left Bautista at the back of the prototype pack - which is only 11 bikes this weekend with the injured Karel Abraham's Cardion Ducati absent.
Aspar's Randy de Puniet and Aleix Espargaro led the CRT field.
1. Jorge Lorenzo Yamaha 1m48.131s
2. Casey Stoner Repsol Honda 1m48.649s + 0.518
3. Dani Pedrosa Repsol Honda 1m48.877s + 0.746
4. Nicky Hayden Ducati 1m48.981s + 0.850
5. Cal Crutchlow Yamaha Tech 3 1m49.023s + 0.892
6. Andrea Dovizioso Yamaha Tech 3 1m49.038s + 0.907
7. Valentino Rossi Ducati 1m49.074s + 0.943
8. Hector Barbera Pramac Ducati 1m49.166s + 1.035
9. Ben Spies Yamaha 1m49.398s + 1.267
10. Stefan Bradl LCR Honda 1m49.438s + 1.307
11. Alvaro Bautista Honda Gresini 1m49.688s + 1.557
12. Randy De Puniet Power Electronics Aspar 1m50.949s + 2.818
13. Aleix Espargaro Power Electronics Aspar 1m51.101s + 2.970
14. Mattia Pasini Speed Master 1m51.253s + 3.122
15. Michele Pirro Honda Gresini 1m51.835s + 3.704
16. Yonny Hernandez Avintia Blusens 1m51.973s + 3.842
17. Colin Edwards NGM Mobile Forward Racing 1m52.154s + 4.023
18. Danilo Petrucci Came IodaRacing Project 1m52.952s + 4.821
19. James Ellison Paul Bird Motorsport 1m53.390s + 5.259
20. Ivan Silva Avintia Blusens 1m53.931s + 5.800